[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,763] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d10123f-a6f0-4ad4-abde-94ff64874827/GCF_008084905.1_ASM808490v1_genomic.fna.gz | prodigal -d GCF_008084905.1_ASM808490v1_genomic.fna/cds.fna -a GCF_008084905.1_ASM808490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:13,180] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:13,180] [INFO] Task started: HMMsearch
[2024-01-24 11:05:13,180] [INFO] Running command: hmmsearch --tblout GCF_008084905.1_ASM808490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/reference_markers.hmm GCF_008084905.1_ASM808490v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:13,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:13,458] [INFO] Found 6/6 markers.
[2024-01-24 11:05:13,490] [INFO] Query marker FASTA was written to GCF_008084905.1_ASM808490v1_genomic.fna/markers.fasta
[2024-01-24 11:05:13,490] [INFO] Task started: Blastn
[2024-01-24 11:05:13,490] [INFO] Running command: blastn -query GCF_008084905.1_ASM808490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/reference_markers.fasta -out GCF_008084905.1_ASM808490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:14,216] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:14,219] [INFO] Selected 26 target genomes.
[2024-01-24 11:05:14,219] [INFO] Target genome list was writen to GCF_008084905.1_ASM808490v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:14,226] [INFO] Task started: fastANI
[2024-01-24 11:05:14,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d10123f-a6f0-4ad4-abde-94ff64874827/GCF_008084905.1_ASM808490v1_genomic.fna.gz --refList GCF_008084905.1_ASM808490v1_genomic.fna/target_genomes.txt --output GCF_008084905.1_ASM808490v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:31,060] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:31,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:31,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:31,075] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:31,075] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:31,075] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	80.5526	600	990	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	78.4675	325	990	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	78.4328	415	990	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	78.3893	328	990	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	78.3735	376	990	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.2993	400	990	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.2883	367	990	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	78.2576	332	990	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1949	372	990	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.0309	291	990	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.9712	300	990	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.9557	285	990	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	77.9372	287	990	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.9232	283	990	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.9192	277	990	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.9013	276	990	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.8655	279	990	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.8285	269	990	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.8208	237	990	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.8158	270	990	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7923	258	990	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.7754	288	990	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.6532	281	990	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.5911	260	990	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.5714	240	990	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1996	217	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:31,078] [INFO] DFAST Taxonomy check result was written to GCF_008084905.1_ASM808490v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:31,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:31,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:31,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/checkm_data
[2024-01-24 11:05:31,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:31,114] [INFO] Task started: CheckM
[2024-01-24 11:05:31,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008084905.1_ASM808490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008084905.1_ASM808490v1_genomic.fna/checkm_input GCF_008084905.1_ASM808490v1_genomic.fna/checkm_result
[2024-01-24 11:05:56,684] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:56,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:56,696] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:56,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:56,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008084905.1_ASM808490v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:56,697] [INFO] Task started: Blastn
[2024-01-24 11:05:56,697] [INFO] Running command: blastn -query GCF_008084905.1_ASM808490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05ef571b-91b0-4c27-8726-24fa22ab37db/dqc_reference/reference_markers_gtdb.fasta -out GCF_008084905.1_ASM808490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:57,680] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:57,682] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:57,682] [INFO] Target genome list was writen to GCF_008084905.1_ASM808490v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:57,687] [INFO] Task started: fastANI
[2024-01-24 11:05:57,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d10123f-a6f0-4ad4-abde-94ff64874827/GCF_008084905.1_ASM808490v1_genomic.fna.gz --refList GCF_008084905.1_ASM808490v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008084905.1_ASM808490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:04,054] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:04,061] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:04,061] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_008084905.1	s__Xanthomarina maritima	100.0	985	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148645.1	s__Xanthomarina spongicola	84.1628	754	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	82.066	731	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	81.9033	500	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	80.7166	654	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	80.5539	600	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_014641635.1	s__Aquaticitalea lipolytica	78.5555	358	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	78.5064	408	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.2266	330	990	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:04,062] [INFO] GTDB search result was written to GCF_008084905.1_ASM808490v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:04,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:04,066] [INFO] DFAST_QC result json was written to GCF_008084905.1_ASM808490v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:04,066] [INFO] DFAST_QC completed!
[2024-01-24 11:06:04,066] [INFO] Total running time: 0h1m0s